Genome-level and transcriptome-level information cannot accurately reflect proteome-level information because post-transcriptional regulations modulate gene expression, because protein post-translational modifications (PTMs) influence protein function, and because most proteins in cells function as complexes with proteins, RNAs, metals or other small molecules. Characterization of the proteome is imperative to understand the roles played by proteins, protein PTMs and even protein complexes in development and diseases.<br/>Top-down proteomics is a well-known strategy for large-scale characterization of proteome at the intact protein level and is very useful for high-resolution characterization of proteoforms that represent all kinds of protein molecules derived from the same gene due to gene-level variations, RNA-level alternative splicing, and protein-level PTMs.[1] The number of proteoforms in human proteome has been estimated to be over 1 million.[2] High-capacity separation of proteoforms before electrospray ionization-mass spectrometry and tandem mass spectrometry (ESI-MS and MS/MS) is essential for deep and high-resolution top-down proteomics.<br/>The top-down proteomics community has made tremendous efforts in improving liquid chromatography (LC)-MS and MS/MS for top-down proteomics. We argue that capillary zone electrophoresis (CZE)-MS and MS/MS is another powerful tool for top-down proteomics because CZE can approach high-capacity separation of intact proteins and because CZE-MS has shown higher sensitivity than LC-MS for protein detection.[3] In my talk, I will talk about our recent work on boosting CZE-MS and MS/MS for large-scale and highly sensitive top-down proteomics.[4,5] I will also introduce our work on developing CZE-MS and MS/MS methodologies for native top-down proteomics that aims to characterize the endogenous protein complexes in cells in discovery mode.[6]<br/>

Denaturing and native top-down proteomics using capillary electrophoresis-tandem mass spectrometry

2019 Fall National Meeting

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